How do you apply rhyme scheme to a poem?

In the study of poetry, you don't really "apply" a rhyme scheme to a poem, rather your job is to identify the rhyme scheme (if there is one) and then talk about its impact. This is normally done by nominating a letter for each "rhyme" within the poem. Let's take Sonnet 116 by Shakespeare as an example (watch out for the letters at the end of the lines):

Let me not to the marriage of true minds  A

Admit impediments. Love is not love 

B Which alters when it alteration finds,  A

Or bends with the remover to remove:  B

O no! it is an ever-fixed mark  C

That looks on tempests and is never shaken;  D

It is the star to every wandering bark,  C

Whose worth's unknown, although his height be taken. D Love's not Time's fool, though rosy lips and cheeks E

Within his bending sickle's compass come: F

Love alters not with his brief hours and weeks, E

But bears it out even to the edge of doom. F

If this be error and upon me proved, G

I never writ, nor no man ever loved. G

 Therefore, with this poem, you would say that it had a regular ABABCDCDEFEFGG rhyme scheme - typical of Shakespeare and his sonnets.